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comparison fuma.xml @ 5:a5f10935f9ab draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 18ae9555a548d5cb3b3d15d46f57c28112bb16b9
author yhoogstrate
date Fri, 20 Nov 2015 11:14:43 -0500
parents cb0543909e83
children ec04b7552167
comparison
equal deleted inserted replaced
4:cb0543909e83 5:a5f10935f9ab
33 -m 33 -m
34 $params.matching_method 34 $params.matching_method
35 35
36 $params.strand_specific_matching 36 $params.strand_specific_matching
37 $params.acceptor_donor_order_specific_matchig 37 $params.acceptor_donor_order_specific_matchig
38
39 --long-gene-size $params.long_gene_size
38 40
39 -a 41 -a
40 $gene_annotations_str 42 $gene_annotations_str
41 -s 43 -s
42 $samples_str 44 $samples_str
83 <option value="preSet" selected="true">Use Defaults</option> 85 <option value="preSet" selected="true">Use Defaults</option>
84 <option value="full">Full parameter list</option> 86 <option value="full">Full parameter list</option>
85 </param> 87 </param>
86 <when value="preSet"> 88 <when value="preSet">
87 <param name="strand_specific_matching" type="hidden" value="--strand-specific-matching" /> 89 <param name="strand_specific_matching" type="hidden" value="--strand-specific-matching" />
88 <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--acceptor-donor-order-specific-matching" /> 90 <param name="acceptor_donor_order_specific_matchig" type="hidden" value="--no-acceptor-donor-order-specific-matching" />
91 <param name="long_gene_size" type="hidden" value="200000" />
89 </when> 92 </when>
90 <when value="full"> 93 <when value="full">
91 <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative"> 94 <param name="matching_method" type="select" label="Matching method: technique used to match fusion genes based on annotated gene sets" help="Overlap is the most sensitive but also more sensitive for long gene artefacts; subset is the recommended technique and EGM is conservative">
92 <option value="overlap">Overlap</option> 95 <option value="overlap">Overlap</option>
93 <option value="subset" selected="True">Subset</option> 96 <option value="subset" selected="True">Subset</option>
103 truevalue="--acceptor-donor-order-specific-matching" 106 truevalue="--acceptor-donor-order-specific-matching"
104 falsevalue="--no-acceptor-donor-order-specific-matching" 107 falsevalue="--no-acceptor-donor-order-specific-matching"
105 label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)" 108 label="Consider fusion genes distinct when the donor and acceptor sites are swapped (A,B) != (B,A)"
106 help="This settings is not recommended when fusion genes detected in DNA-Seq are used" /> 109 help="This settings is not recommended when fusion genes detected in DNA-Seq are used" />
107 110
111 <param name="long_gene_size" type="integer" min="0" value="200000" label="Long gene size" help="Gene-name based matching is more sensitive to long genes. This is the gene size used to mark fusion genes spanning a 'long gene' as reported the output. Use 0 to disable this feature (--long-gene-size)" />
112
108 <param name="output_format" type="select" label="Output format"> 113 <param name="output_format" type="select" label="Output format">
109 <option value="list_boolean" selected="true">List (Boolean)</option> 114 <option value="list_boolean" selected="true">List (Boolean)</option>
110 <option value="list">List</option> 115 <option value="list">List</option>
111 <option value="summary">Count summary</option> 116 <option value="summary">Count summary</option>
112 </param> 117 </param>
144 <param name="settingsType" value="full" /> 149 <param name="settingsType" value="full" />
145 150
146 <param name="matching_method" value="subset" /> 151 <param name="matching_method" value="subset" />
147 <param name="strand_specific_matching" value="--strand-specific-matching" /> 152 <param name="strand_specific_matching" value="--strand-specific-matching" />
148 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" /> 153 <param name="acceptor_donor_order_specific_matchig" value="--acceptor-donor-order-specific-matching" />
154 <param name="long_gene_size" value="200000" />
149 <param name="output_format" value="list_boolean" /> 155 <param name="output_format" value="list_boolean" />
150 156
151 <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" /> 157 <output name="fuma_overview" file="edgren_test_01_specifc_matching_output.txt" />
152 </test> 158 </test>
153 <test> 159 <test>
175 <param name="settingsType" value="full" /> 181 <param name="settingsType" value="full" />
176 182
177 <param name="matching_method" value="subset" /> 183 <param name="matching_method" value="subset" />
178 <param name="strand_specific_matching" value="False" /><!-- Set to false, automatically sets the false value --> 184 <param name="strand_specific_matching" value="False" /><!-- Set to false, automatically sets the false value -->
179 <param name="acceptor_donor_order_specific_matchig" value="False" /><!-- Set to false, automatically sets the false value --> 185 <param name="acceptor_donor_order_specific_matchig" value="False" /><!-- Set to false, automatically sets the false value -->
186 <param name="long_gene_size" value="200000" />
180 <param name="output_format" value="list_boolean" /> 187 <param name="output_format" value="list_boolean" />
181 188
182 <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" /> 189 <output name="fuma_overview" file="edgren_test_02_unspecifc_matching_output.txt" />
183 </test> 190 </test>
184 </tests> 191 </tests>